+Under development!
+
+This contains documentation, tutorials, and examples for [https://sites.google.com/site/cmzmasek/home/software/forester/ forester].
+
+Documentation for [https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/ Archaeopteryx] can be found [https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation here].
+
+*All examples require jar-file "forester.jar" to be in the class-path.*
+
+Download: http://code.google.com/p/forester/downloads/list
+
+Author: [https://sites.google.com/site/cmzmasek/ Christian Zmasek], Sanford-Burnham Medical Research Institute
+
+
+Copyright (C) 2013 Christian M Zmasek. All rights reserved.
+
+
+
+= Reading and writing of phylogenetic trees =
+
+
+
+{{{
+
+package examples;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.util.ForesterUtil;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Reading-in of (a) tree(s) from a file.
+ final File treefile = new File( "/path/to/tree.xml" );
+ PhylogenyParser parser = null;
+ try {
+ parser = ParserUtils.createParserDependingOnFileType( treefile, true );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ Phylogeny[] phys = null;
+ try {
+ phys = PhylogenyMethods.readPhylogenies( parser, treefile );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ // Writing trees to a file.
+ final File outfile = new File( "/path/to/out_tree.xml" );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ }
+}
+
+}}}
+
+
+
+= Reading of phylogenetic trees and displaying them with Archaeopteryx =
+
+
+{{{
+
+package examples;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Reading-in of (a) tree(s) from a file.
+ final File treefile = new File( "/path/to/tree.xml" );
+ PhylogenyParser parser = null;
+ try {
+ parser = ParserUtils.createParserDependingOnFileType( treefile, true );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ Phylogeny[] phys = null;
+ try {
+ phys = PhylogenyMethods.readPhylogenies( parser, treefile );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ // Display of the tree(s) with Archaeopteryx.
+ Archaeopteryx.createApplication( phys );
+ }
+}
+
+}}}
+
+
+
+
+= Creating a new tree and displaying it with Archaeopteryx =
+
+
+{{{
+
+package examples;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Creating a new rooted tree with two external nodes.
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode root = new PhylogenyNode();
+ final PhylogenyNode d1 = new PhylogenyNode();
+ final PhylogenyNode d2 = new PhylogenyNode();
+ root.setName( "root" );
+ d1.setName( "descendant 1" );
+ d2.setName( "descendant 2" );
+ root.addAsChild( d1 );
+ root.addAsChild( d2 );
+ phy.setRoot( root );
+ phy.setRooted( true );
+ // Displaying the newly created tree with Archaeopteryx.
+ Archaeopteryx.createApplication( phy );
+ }
+}
+
+}}}
+
+
+
+
+
+
+= Using iterators to visit tree nodes in certain orders =
+
+{{{
+
+package examples;
+
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Creating a new rooted tree with four external nodes.
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode root = new PhylogenyNode();
+ final PhylogenyNode d1 = new PhylogenyNode();
+ final PhylogenyNode d2 = new PhylogenyNode();
+ final PhylogenyNode d11 = new PhylogenyNode();
+ final PhylogenyNode d12 = new PhylogenyNode();
+ root.setName( "root" );
+ d1.setName( "1" );
+ d2.setName( "2" );
+ d11.setName( "1-1" );
+ d12.setName( "1-2" );
+ root.addAsChild( d1 );
+ root.addAsChild( d2 );
+ d2.addAsChild( d11 );
+ d2.addAsChild( d12 );
+ phy.setRoot( root );
+ phy.setRooted( true );
+ // Using a variety of iterators to visit the nodes of the newly created tree.
+ System.out.println( "post-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "pre-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "level-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorLevelOrder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "external nodes only:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ }
+}
+
+}}}
+
+
+
+
+
+
+
+
+
+= Creating a basic gene tree (with branch lengths) =
+
+
+{{{
+
+package examples;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Creating a new rooted tree with two external nodes.
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode root = new PhylogenyNode();
+ final PhylogenyNode d1 = new PhylogenyNode();
+ final PhylogenyNode d2 = new PhylogenyNode();
+ // Setting of distances.
+ d1.setDistanceToParent( 1.2 );
+ d2.setDistanceToParent( 2.4 );
+ // Adding species information.
+ final Taxonomy t1 = new Taxonomy();
+ t1.setScientificName( "Nematostella vectensis" );
+ d1.getNodeData().addTaxonomy( t1 );
+ final Taxonomy t2 = new Taxonomy();
+ t2.setScientificName( "Monosiga brevicollis" );
+ d2.getNodeData().addTaxonomy( t2 );
+ // Adding gene names.
+ final Sequence s1 = new Sequence();
+ s1.setName( "Bcl-2" );
+ d1.getNodeData().addSequence( s1 );
+ final Sequence s2 = new Sequence();
+ s2.setName( "Bcl-2" );
+ d2.getNodeData().addSequence( s2 );
+ // Root is a speciation.
+ final Event ev = new Event();
+ ev.setSpeciations( 1 );
+ ev.setDuplications( 0 );
+ root.getNodeData().setEvent( ev );
+ // Putting the tree together.
+ root.addAsChild( d1 );
+ root.addAsChild( d2 );
+ phy.setRoot( root );
+ phy.setRooted( true );
+ // Displaying the newly created tree with Archaeopteryx.
+ Archaeopteryx.createApplication( phy );
+ }
+}
+
+}}}
+
+= Writing a phylogenetic tree to a graphics file (e.g. png, jpg) =
+
+{{{
+
+package examples;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.Options;
+import org.forester.archaeopteryx.TreeColorSet;
+
+public class phylo2graphics {
+
+ public static void main( final String[] args ) {
+ try {
+ final Configuration config = new Configuration();
+ // Could also read a configuration file with:
+ // Configuration config = new Configuration("my_configuration_file.txt", false, false, false);
+ config.putDisplayColors( TreeColorSet.BACKGROUND, new Color( 255, 255, 255 ) );
+ config.putDisplayColors( TreeColorSet.BRANCH, new Color( 0, 0, 0 ) );
+ config.putDisplayColors( TreeColorSet.TAXONOMY, new Color( 0, 0, 0 ) );
+ config.setPhylogenyGraphicsType( Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ AptxUtil.writePhylogenyToGraphicsFile( new File( "my_tree.xml" ),
+ new File( "my_tree_graphics.png" ),
+ 1000,
+ 1000,
+ GraphicsExportType.PNG,
+ config );
+ // If the tree 'phy' already exists, can also use this:
+ AptxUtil.writePhylogenyToGraphicsFile( phy,
+ new File( "out.png" ),
+ 1000,
+ 1000,
+ GraphicsExportType.PNG,
+ config );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+}
+
+}}}
+
+= Setting node/branch colors of a phylogenetic tree and writing it to a graphics file =
+
+{{{
+
+package examples;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.Options;
+import org.forester.archaeopteryx.TreeColorSet;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchColor;
+import org.forester.phylogeny.data.BranchWidth;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;